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HIV-1 phylogeny during suppressive antiretroviral therapy

Bale, Michael J.; Kearney, Mary F.

Current Opinion in HIV and AIDS: May 2019 - Volume 14 - Issue 3 - p 188–193
doi: 10.1097/COH.0000000000000535
PHYLOGENETICS IN HIV TRANSMISSION: Edited by Morgane Rolland and Josh Herbeck

Purpose of review Studies of HIV-1 genetic diversity can provide clues on the effect of antiretroviral therapy (ART) on viral replication, the mechanisms for viral persistence, and the efficacy of new interventions. This article reviews methods for interrogating intrahost HIV-1 diversity, addresses the ongoing debate regarding HIV-1 compartmentalization and replication during ART, and summarizes recent findings on the effects of curative strategies on HIV-1 populations.

Recent findings HIV-1 replication in the blood is virtually halted upon the initiation of ART. However, proliferation of cells infected prior to ART provides a self-renewing reservoir for infection during ART. Current evidence supports that proliferation of infected cells is a mechanism for HIV-1 persistence in both the blood and the tissues. However, more studies are required to determine if tissue sanctuaries exist that may also allow viral replication during ART. Recent studies investigating potential curative interventions show little effect on the genetic landscape of HIV-1 infection and highlight the need to develop strategies targeting the proliferation of infected cells.

Summary Using phylogeny to characterize HIV-1 genetic diversity and evolution during ART has demonstrated a lack of viral replication, the proliferation of infected cells, and provides one metric to measure the effect of new interventions aimed at achieving a functional cure for HIV-1.

HIV Dynamics and Replication Program, CCR, National Cancer Institute (NCI), Frederick, Maryland, USA

Correspondence to Michael J. Bale, HIV Dynamics and Replication Program, NCI-Frederick, 1050 Boyles St., Bldg. 535, Frederick, MD 21702, USA. E-mail:

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